| "Perfidious machiavellian friar" : Florence Conry's campaign for a Catholic restoration in Ireland, 1592-1616 | O'Connor, Thomas | Article in Journal | | 2002 |
| A justification for foreign intervention in early modern Ireland | O'Connor, Thomas | Article in Book | | 2003 |
| A theology thesis defended by an Irish clerical student in Paris in 1739 | | Article in Journal | | 1997 |
| An Irish Jansenist in seventeenth-century France : John Callaghan 1605-54 | O'Connor, Thomas | Monograph or Collective Volume | National University of Ireland | 2005 |
| An Irish theologian in enlightenment France : Luke Joseph Hooke, 1714-96 | O'Connor, Thomas | Monograph or Collective Volume | Columba | 1995 |
| Aspects of the role of the Holy Office in Irish church affairs in the early seventeenth century | O'Connor, Thomas | Article in Book | | 2009 |
| Boston Catholics : a history of the church and its people | O'Connor, Thomas H., 1922-2012 | Monograph or Collective Volume | Northeastern University Press | 1998 |
| Catholic and Protestant Dublin weavers before the Spanish Inquisition, 1745-54 | O'Connor, Thomas | Article in Book | | 2016 |
| Catholic archives of the United States | O'Connor, Thomas F. | Article in Journal | | 1946 |
| College communities abroad : Education, migration and Catholicism in early modern Europe | | Monograph or Collective Volume | Manchester University Press | 2017 |
| Confessional to-ing and fro-ing in the eighteenth-century diaspora : Helena Barry's story (1738) | O'Connor, Thomas | Article in Book | | 2015 |
| Custom, authority and tolerance in Irish political thought : David Rothe's Analecta Sacra et Mira (1616) | O'Connor, Thomas | Article in Book | | 2009 |
| Custom, authority, and tolerance in Irish political thought : David Rothe's Analecta Sacra et Mira (1616) | O'Connor, Thomas | Article in Journal | | 2000 |
| David Rothe, bishop of Ossory (c.1573-1650): bishop and historian | O'Connor, Thomas | Article in Journal | | 2009 |
| Diplomatic preparations for Kinsale | O'Connor, Thomas | Article in Book | | 2002 |
| Directories as genealogical sources for county Kerry | O'Connor, Thomas, of County Kerry | Article in Journal | | 1991 |
| Disputes in the Irish college, Douai (1594–1614) | O'Connor, Thomas | Article in Journal | | 2019 |
| Dying to the old, rising to the new : an Icelandic saga with an Irish twist | O'Connor, Thomas | Article in Book | | 2016 |
| Entre Castigo y asimilación : los irlandeses y la Inquisición espanola (1580-1750) | O'Connor, Thomas | Article in Book | | 2014 |
| Exile Movement: Male Institutions, 1568-1640 | O'Connor, Thomas | Article in Book | | 2023 |
| Exile, astrology and the Spanish Inquisition | O'Connor, Thomas | Article in Book | | 2013 |
| Fitzpatrick's Boston, 1846-1866 : John Bernard Fitzpatrick, third bishop of Boston | O'Connor, Thomas H. | Monograph or Collective Volume | Northeastern UP | 1984 |
| Forming Catholic Communities: Irish, Scots and English College networks in Europe, 1568–1918 | | Monograph or Collective Volume | BRILL | 2018 |
| Griffith’s valuation a genealogical source for county Kerry | O'Connor, Thomas, of County Kerry | Article in Journal | | 1995 |
| Hugh O'Neill : free spirit, religious chameleon or ardent Catholic? | O'Connor, Thomas | Article in Book | | 2004 |
| Introduction | Lyons, Mary AnnO'Connor, Thomas | Article in Book | | 2006 |
| Introduction | Lyons, Mary Ann,O'Connor, Thomas, | Article in Book | | 2010 |
| Ireland and Europe, 1580-1815 : some historiographical remarks | O'Connor, Thomas | Article in Book | | 2001 |
| Irish communities in early-modern Europe | | Monograph or Collective Volume | Four Courts | 2006 |
| Irish Franciscan networks at home and aborad, 1607-1640 | O'Connor, Thomas | Article in Book | | 2010 |
| Irish Jansenists, 1600-70 : religion and politics in Flanders, France, Ireland and Rome | O'Connor, Thomas | Monograph or Collective Volume | Four Courts | 2008 |
| Irish migrants in Europe after Kinsale, 1602-1820 | | Monograph or Collective Volume | Four Courts | 2003 |
| Irish migration to Spain and the formation of an Irish college network, 1589-1800 | O'Connor, Thomas | Article in Book | | 2001 |
| Irish voices from the Spanish Inquisition : migrants, converts and brokers in early modern Iberia | O'Connor, Thomas | Monograph or Collective Volume | Palgrave Macmillan | 2016 |
| Irish votes and Yankee cotton : the constitution of 1853 | O'Connor, Thomas H. | Article in Journal | | 1983 |
| John A. McClelland 1870-1920 | O'Connor, Thomas | Article in Book | | 2003 |
| Killarney tourist literature of the past | O'Connor, Thomas, of County Kerry | Article in Journal | | 1994 |
| Luke Joseph Hooke 1714-96 : an Irish theologian in enlightenment France, 1714-96 | O'Connor, Thomas | Monograph or Collective Volume | Four Courts | 1995 |
| Luke Wadding's networks at home and abroad | O'Connor, Thomas | Article in Book | | 2008 |
| Marsh's library and the Irish Catholic tradition | O'Connor, Thomas | Article in Book | | 2004 |
| Obituary. Patrick J. Corish 1921-2013 | O'Connor, Thomas | Article in Journal | | 2014 |
| Prequels: the Irish European diaspora | O'Connor, Thomas | Article in Book | | 2019 |
| Problems with databases and the XML solution | Clancy, DenisKeating, John G.Lyons, Mary AnnO'Connor, Thomas | Article in Journal | | 2004 |
| Religion and identity - the Irish dillema | O'Connor, Thomas | Article in Journal | | 1999 |
| Religious change, 1550-1800 | O'Connor, Thomas | Article in Book | | 2006 |
| Scottish comunities abroad : Some concluding remarks | O'Connor, ThomasSogner, SølviVan Voss, Lex Heerma | Article in Book | | 2005 |
| Strangers to citizens : the Irish in Europe, 1600-1800 | Lyons, Mary AnnO'Connor, Thomas | Monograph or Collective Volume | National Library of Ireland | 2008 |
| Surviving the Civil Constitution of the Clergy : Luke Joseph Hooke's revolutionary experiences | O'Connor, Thomas | Article in Journal | | 1996 |
| The Boston Irish : a political history | O'Connor, Thomas H. | Monograph or Collective Volume | North Eastern University Press | 1995 |
| The Catholic Church and Catholics in an era of sanctions and restraints, 1690–1790 | O'Connor, Thomas | Article in Book | | 2018 |
| The difficulties in coping with parish registers as a genaelogical source | O'Connor, Thomas, of County Kerry | Article in Journal | | 1992 |
| The domestic and international roles of Irish overseas colleges, 1590-1800 | O'Connor, Thomas | Article in Book | | 2017 |
| The Irish in Boston | O'Connor, Thomas H. | Article in Journal | | 1979 |
| The Irish in Europe, 1580-1815 | | Monograph or Collective Volume | Four Courts | 2001 |
| The Irish in New England | O'Connor, Thomas H. | Article in Journal | | 1985 |
| The Irish in New England | O'Connor, Thomas H. | Monograph or Collective Volume | New England Historic Genealogical Society | 1985 |
| The Irish in New England | O'Connor, Thomas H. | Article in Book | | 1985 |
| The role of Irish clerics in Paris University politics 1730-40 | O'Connor, Thomas | Article in Journal | | 1999 |
| The tithe applotment books as a Co. Kerry genealogical source | O'Connor, Thomas, of County Kerry | Article in Journal | | 1996 |
| The Ulster earls and baroque Europe : refashioning Irish identities, 1600-1800 | | Monograph or Collective Volume | Four Courts | 2009 |
| the wages of bigamy (1663) | O'Connor, Thomas | Article in Book | | 2019 |
| Thomas Messingham (c.1575-1638?) and the seventeenth-century church | O'Connor, Thomas | Article in Journal | | 2000 |
| Towards the invention of the Irish Catholic natio : Thomas Messingham's Florilegium (1624) | O'Connor, Thomas | Article in Journal | | 1999 |